Groundwater is an important resource in Ireland which is under increasing risk from the burgeoning numbers of decentralized houses and their respective on-site treatment systems which discharge effluent to ground via a number of parallel percolation trenches. The three-dimensional performance of separate percolation areas have been intensively monitored to ascertain the attenuation of selected Endocrine Disruption Compounds (EDCs) from freely draining unsaturated subsoils receiving septic tank effluent and secondary treated effluent. The performance of secondary treatment and tertiary treatment horizontal subsurface flow reed beds was also studied with respect to EDC removal. The study showed that the development of a biomat across the percolation areas receiving secondary treated effluent was muted compared to the site receiving septic tank effluent on which the percolating effluent spread naturally by gravity over a much larger area. In general, the results showed the oestrogens (oestrone, oestrdiaol, ethynyloestradiol, and oestriol) percolating though the unsaturated subsoil were significantly degraded with depth down to very low values (<1 ng/L), with the exception of oestriol in the secondary treated effluent plume which seemed to be more persistent. There appeared to be little or no degradation of oestrogens under the saturated anaerobic conditions in the reed beds. The organic oxygen compound, bisphenol A, was not significantly reduced in the aerobic secondary treatment processes although some degradation was evident with depth through the subsoil in all trenches. Bisphenol A also showed no significant degradation in the reed bed environment. Finally, the study investigated the fate of caffeine (as a potential indicator of on-site effluent) which showed considerable removal in the aerobic subsoil conditions beneath all the trenches compared to little degradation of caffeine in the saturated anaerobic environment of the reed beds.